BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0005.0291.p (298 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313839|ref|YP_003777931.1| MetE/MetH family transcription ... 533 e-153 gi|300312961|ref|YP_003777053.1| transcription regulator protein... 84 2e-17 gi|300309864|ref|YP_003773956.1| LysR family transcription regul... 79 5e-16 gi|300313217|ref|YP_003777309.1| LysR family transcription regul... 78 1e-15 gi|300313131|ref|YP_003777223.1| LysR family transcription regul... 77 2e-15 >gi|300313839|ref|YP_003777931.1| MetE/MetH family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 295 Score = 533 bits (1372), Expect = e-153, Method: Compositional matrix adjust. Identities = 257/284 (90%), Positives = 272/284 (95%) Query: 10 SIVQEVEKQGSLTAAAGVLHVTQSALSHSMKKLEQQLGTDIWLREGRSLRLTQAGQYLLA 69 SIVQEVE+QGSLTAAAGVLHVTQSALSHSMKKLEQQLGTDIWLREGR LRLTQAGQYLLA Sbjct: 8 SIVQEVERQGSLTAAAGVLHVTQSALSHSMKKLEQQLGTDIWLREGRHLRLTQAGQYLLA 67 Query: 70 VANRVLPQLNLAEERLQQFAQGERGALRIGMECHPCYQWLLKVVSPYLAAWPDVDVDVKQ 129 VANRVLPQL+LAEERL+QFAQGERGALRIGMECHPCYQWLLKVVSPYLAAWPDVDVDVKQ Sbjct: 68 VANRVLPQLSLAEERLRQFAQGERGALRIGMECHPCYQWLLKVVSPYLAAWPDVDVDVKQ 127 Query: 130 KFQFGGIGALFGYEIDLLVTPDPLDKPGLVFEPVFDYEQVLVVAGGHKLAKEEYVKPKQL 189 KFQFGGIGALFGYEIDLLVTPDPLDKPGLVFEPVFDYEQVLVVA H LA +YVKP+QL Sbjct: 128 KFQFGGIGALFGYEIDLLVTPDPLDKPGLVFEPVFDYEQVLVVASDHPLADVDYVKPRQL 187 Query: 190 SNEVLVTYPVPVDRLDIYSMFLTPAGITPKRHKPIETTDIMLQMVASGRGVAALPRWLVL 249 SNEVLVTYPVPVDRLDIY+ FL PAGI P+RHK IETTDIMLQMVASGRGVAALPRWLVL Sbjct: 188 SNEVLVTYPVPVDRLDIYTQFLAPAGIVPRRHKTIETTDIMLQMVASGRGVAALPRWLVL 247 Query: 250 EYADKMDVVPVRLGKNGIAKHIFLGARETDVSIDYLRAFIEQAK 293 EYA++M+VVPVRLGK GIAKHI+LGARE+DV IDYLRAFI++A+ Sbjct: 248 EYAEQMEVVPVRLGKQGIAKHIYLGARESDVEIDYLRAFIDEAR 291 >gi|300312961|ref|YP_003777053.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 84.0 bits (206), Expect = 2e-17, Method: Compositional matrix adjust. Identities = 70/269 (26%), Positives = 119/269 (44%), Gaps = 12/269 (4%) Query: 20 SLTAAAGVLHVTQSALSHSMKKLEQQLGTDIWLREGRSLRLTQAGQYLLAVANRVLPQLN 79 S + AA +LH+ Q LS +++LE+ LG ++ R R + LT AG++ +VL +L Sbjct: 17 SFSRAAELLHIAQPPLSRQIRQLEEMLGVELIDRASRPIALTMAGKFFYEQTLQVLSRLE 76 Query: 80 LAEERLQQFAQGERGALRIGMECHPCYQWLLKVVSPYLAAWPDVDVDVKQKFQFGGIGAL 139 EE + A+G + IG Y L +++ + P++++ + + AL Sbjct: 77 QIEEGTRVIARGRQHWFNIGFVPSALYGLLPEMIKRFRTEMPEIEIGFSEIVTMEQVEAL 136 Query: 140 FGYEIDLLVTPDPLDKPGLVFEPVFDYEQVLVVAGGHKLAKEEYVKPKQLSNEVLVTYPV 199 ID+ P+ P +V E + + V V GH L V QL+ + + YP Sbjct: 137 KSGRIDVGFGRLPISDPDIVCETIVEEPLVAVFPLGHPLLARNKVTLAQLAAQRFILYPA 196 Query: 200 P-----VDR-LDIYSMFLTPAGITPKRHKPIETTDIMLQMVASGRGVAALPRWLVLEYAD 253 D+ LDI+S + P K + +VA+G GV +PR ++ Sbjct: 197 RPRPSYADQVLDIFS----SRALRPSIVKEANEMQTAIGLVAAGVGVTLVPRS--VQGLH 250 Query: 254 KMDVVPVRLGKNGIAKHIFLGARETDVSI 282 + DVV L G+ + + R D S+ Sbjct: 251 RSDVVYRPLSNKGVHSPVIMNFRANDRSL 279 >gi|300309864|ref|YP_003773956.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 306 Score = 78.6 bits (192), Expect = 5e-16, Method: Compositional matrix adjust. Identities = 64/241 (26%), Positives = 117/241 (48%), Gaps = 6/241 (2%) Query: 24 AAGVLHVTQSALSHSMKKLEQQLGTDIWLREGRSLRLTQAGQYLLAVANRVLPQLNLAEE 83 AA +L++TQ LS + LE +LG ++ R GR++RLT G+ LA A+R+L AE Sbjct: 22 AAALLNMTQPPLSRQIHLLEHRLGVQLFERVGRTVRLTTEGRVFLADASRLLQLSEQAES 81 Query: 84 RLQQFAQGERGALRIGMECHPCYQWLLKVVSPYLAAWPDVDVDVKQKFQFGGIGALFGYE 143 +++ +QG+ G +R+G Y+ + +++ + P++DV + + + A Sbjct: 82 TVRRASQGKTGRVRVGFTGAAGYELIPELLMQARTSLPEIDVVLFELISVAQLEAFTANT 141 Query: 144 IDL-LVTPDPLDKPGLVFEPVFDYEQVLVVAGGHKLAKEEYVKPKQLSNEVLVTYPVPVD 202 ID+ + P +P L + V + VL + GH LA + + QL + + + P Sbjct: 142 IDIGFLRPVASRQP-LELQLVDEEALVLAMPQGHALAAYDRIATTQLDGQPFIMHS-PTH 199 Query: 203 RLDIYS---MFLTPAGITPKRHKPIETTDIMLQMVASGRGVAALPRWLVLEYADKMDVVP 259 Y L A + P + I+ + +L +V +G GV LP + D+++ P Sbjct: 200 GKYFYERIMAMLGAADVKPDFTQYIDQSHTILSLVRAGLGVGILPASAQRFHYDRVEFRP 259 Query: 260 V 260 + Sbjct: 260 L 260 >gi|300313217|ref|YP_003777309.1| LysR family transcription regulator [Herbaspirillum seropedicae SmR1] Length = 296 Score = 77.8 bits (190), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 75/286 (26%), Positives = 130/286 (45%), Gaps = 17/286 (5%) Query: 11 IVQEVEKQGSLTAAAGVLHVTQSALSHSMKKLEQQLGTDIWLREGRSLRLTQAGQYLLAV 70 I + V +G +T AA L+ QS ++ +K+LEQ +G +++R+ R + LT AG+ LL Sbjct: 17 IFRTVVAEGGVTRAAERLNRVQSNVTTRIKQLEQSMGVPLFVRDRRRMVLTAAGEALLDY 76 Query: 71 ANRVLPQLNLAEERLQQFA-QGERGALRIGMECHPCYQWLLKVVSPYLAAWPDVDVDVKQ 129 A R+ L+LA+E Q A Q RG LRIG L ++ + WP+V +++ Sbjct: 77 AERI---LDLAQEARQAVAPQSPRGRLRIGSMESAAASRLPGPLAEFHQRWPEVRLELST 133 Query: 130 KFQFGGIGALFGYEIDLLVTPDPLDKPGLVFEPVFDYEQVLVVAGGHKLAKEEYVKPKQL 189 + + ++D + P+ P P+F E +LV H+ + P+++ Sbjct: 134 APTDVLMAQVRACKLDAALVAGPVSDPAFDATPLFREELLLVTPRSHRRVR----APEEV 189 Query: 190 SNEVLVTYPVPVD-RLDIYSMFLTPAGITPKRHKP----IETTDIMLQMVASGRGVAALP 244 + L+ + R + F AG R P + + +L V++G GVA +P Sbjct: 190 MLDTLIVFEQGCAYRRHAEAWF---AGHGAGRQLPRTLELASYHAILACVSAGAGVAVVP 246 Query: 245 RWLVLEYADKMDVVPVRLGKNGIAKHIFLGARET-DVSIDYLRAFI 289 R ++ + LG++G + RE S LRA + Sbjct: 247 RSVIAMQMEPHGFATHSLGRDGRITTFLISRRERYSASFLALRALL 292 >gi|300313131|ref|YP_003777223.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 307 Score = 77.0 bits (188), Expect = 2e-15, Method: Compositional matrix adjust. Identities = 70/244 (28%), Positives = 116/244 (47%), Gaps = 10/244 (4%) Query: 11 IVQEVEKQGSLTAAAGVLHVTQSALSHSMKKLEQQLGTDIWLREGRSLRLTQAGQYLLAV 70 V+ VE +G T AA L V QSALS +K+LE L + RE ++ LTQAGQ Sbjct: 10 FVEIVEARG-YTRAAERLFVAQSALSRQIKELEADLDVVLLRREAKTFELTQAGQDFYER 68 Query: 71 ANRVLPQLNLAEERLQQFAQGERGALRIGMECH-PCYQWLLKVVSPYLAAWPDVDVDVKQ 129 + ++L L+ A + + +GE GALR+ P L +++ L A+P + +++ Q Sbjct: 69 SRKILLDLDRAVAQARTIGKGEHGALRLLHSSSVPLTAPLGPMLNEALKAFPGISLEISQ 128 Query: 130 ---KFQFGGIGALFGYEIDLLVTPDPLDKPGLVFEPVFDYEQVLVVAGGHKLAKEEYVKP 186 ++Q I +I L P P L ++ V V GH+LA+ + V+ Sbjct: 129 APSEYQAREI-VEGSADIGLARLPILRANPNLASTVLYRERLVAAVPAGHRLAQRQEVEI 187 Query: 187 KQLSNEVLVTYPVPVDRLDIYSMF---LTPAGITPKRHKPIETTDIMLQMVASGRGVAAL 243 +L +E VT P DR + + G P+ + + +L +V +G G+A + Sbjct: 188 AELRDEFFVTVP-HRDRGGLSYLVAERCIAHGFYPRVARATSRKNSLLSLVNAGFGIAVV 246 Query: 244 PRWL 247 P+ + Sbjct: 247 PQSM 250 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.319 0.136 0.400 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 947,619 Number of extensions: 41780 Number of successful extensions: 212 Number of sequences better than 1.0e-08: 36 Number of HSP's gapped: 206 Number of HSP's successfully gapped: 36 Length of query: 298 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 213 Effective length of database: 1,217,395 Effective search space: 259305135 Effective search space used: 259305135 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 130 (54.7 bits)